ABSTRACTS
Marina Joubert, Stellenbosch University
Communicating about antimicrobial resistance - reflecting on challenges, solutions and social justice concerns
​Public communication about antimicrobial resistance (AMR) is a critical element of global and national strategies to address this escalating health threat. Yet, like AMR itself, efforts to communicate about it face intersecting challenges that limit their effectiveness. This paper presents findings from a scoping review of 88 scholarly manuscripts published between 2015 and 2024, synthesising key insights into AMR communication. We identify nine overarching themes that shape effective public engagement: (1) the role of social science theories, (2) sensitivity to diverse socio-cultural contexts, (3) participatory engagement and dialogue, (4) language and framing, (5) messaging strategies, (6) media platforms and impacts, (7) large-scale campaigns, (8) creative approaches, and (9) evaluation practices. Particular attention is given to the importance of reaching disadvantaged and vulnerable communities. Drawing on these themes, we highlight practical recommendations for researchers, policymakers, and practitioners, advocating a re-imagining of AMR communication as a civic and cultural practice that is reflexive, context-sensitive, and designed to enhance societal relevance and impact.​
Jerolen Naidoo, Council for Scientific and Industrial Research
Transitioning African microbiome research towards real-world impact
The human microbiome is increasingly recognized as a critical driver of health and disease, with global efforts already translating microbiome science into clinical applications such as faecal microbiota transplantation, next-generation probiotics, and microbiome-based diagnostics. While these innovations are advancing rapidly in high-income countries, their translation within Africa remains limited despite the continent’s unique microbial diversity and pressing health challenges. South Africa has established early momentum, with research initiatives linking microbiome profiles to infectious diseases, metabolic disorders, and host–environment interactions. However, barriers such as limited infrastructure, underrepresentation of African cohorts in global datasets, regulatory uncertainty, and lack of coordinated industry partnerships constrain real-world implementation. This presentation will explore how African-led microbiome research can move beyond academic discovery towards tangible health and economic impact. Opportunities include leveraging Africa’s unique cohorts to generate globally relevant insights, fostering biotech spin-outs around microbiome-based diagnostics and therapeutics, and aligning research outputs with public health priorities. By addressing systemic challenges and building sustainable innovation pipelines, African microbiome science can not only close global knowledge gaps but also deliver context-specific solutions for health systems, patients, and industries on the continent.
Jan Baedke, Ruhr University Bochum
The environment of the microbiome: Methodological and ethical challenges
In recent years, the microbiome has become a key focus in biological and biomedical research. Studies show the human microbiome is linked to autoimmune, respiratory, and metabolic disorders. They suggest that biological normality emerges from complex interactions between organisms and their environmental and social conditions. By focusing on case studies of human microbiome ecology on indigenous populations, especially projects like the Microbiota Vault that aim to conserve microbiota of indigenous groups for biomedical purposes, I discuss methodological and ethical challenges of this research when collecting, processing, and storing microbial data from socio-cultural environments. This includes (i) identifying the epistemic and non-epistemic values that underly conceptualizations of environments as external (i.e. environments are in some way causally decoupled from the actions of the host) or constructed (i.e. host and its surroundings are reciprocally interrelated). Based on each conceptual framework, I show that (ii) researchers adopt different microbes sampling protocols, interact with target populations differently, and store data differently. Finally, (iii) a number of ethical problems are discussed. This includes, for example, to avoid objectifying indigenous bodies from which ‘healthy microbes’ are collected (especially in externalist approaches that decouple microbes from hosts, to whom researchers then have no moral obligations); or to prevent intensive long-time sampling from multiple body sides to be invasive and culturally inappropriate (especially in views of complex co-constructed and permanently changing environments). More generally, obstacles to developing clearer ethical guidelines are discussed that include strengthening indigenous rights and data ownership.
Jack Jansma, Stellebosch University
Challenges and opportunities for global south leadership in microbiota research
The recent surge in microbiota-related research has led to a better understanding of the relationship between us and the micro-organisms living in our intestine, called the gut microbiota. Furthermore, investigating our gut microbiota has resulted in the identification and prevention of microbiota related disorders and opened the door for the development of microbiota-targeted interventions. However, our understanding of the interplay between host and microbiota is hampered by technical, effort-based and conceptual challenges. Due to the inherently technical nature of microbiota-related research, it utilizes large datasets, requires expensive equipment and data handling, researchers in the global south face an additional set of challenges. Modern microbiota research is relatively new and still developing. For example, current databases are skewed towards populations in the global north, even though the vast majority of people worldwide live in the global south. Moreover, the composition and function of our microbiota is driven by lifestyle, genetics and environmental factors, limiting the applicability of most studies on populations living in the global south. Here, we discuss science wide issues related to the global south such as helicopter science and specifically focus on challenges facing microbiota-related research in the global south. We discuss current efforts to resolve these issues such as tried in the AWI-Gen 2 Microbiome project [1] and take inspiration from macro ecologists based in South Africa [2]. We highlight the need for regional researchers, regional policymakers and regional communities to come together to share resources and take the lead in filling the data gap, form a strong network, encourage collaboration across multiple disciplines and establish a regional knowledge base. Researchers in the global south are in a unique position to play an important role in addressing current challenges and moving the whole microbiota field forward, provided that general issues related to helicopter science practices are addressed simultaneously.
References
1. Maghini DG et al. Expanding the human gut microbiome atlas of Africa. Nature 2025 638:8051 2025;638:718–728. https://doi.org/10.1038/s41586-024-08485-8
2. MacFadyen S et al. Drowning in data, thirsty for information and starved for understanding: A biodiversity information hub for cooperative environmental monitoring in South Africa. Biol Conserv 2022;274:109736. https://doi.org/10.1016/J.BIOCON.2022.109736
Herbert Sina Bio (University of Abomey-Calavi) & Andrea Butcher (University of Helsinki
Navigating incongruous but interpenetrating worlds: lessons for a decolonial microbiome research from Benin
This chapter engages with the dilemma of inclusive human diversity in microbiome databases from the position of onto-epistemics and knowledge guardianship in West African medical systems. We are a multidisciplinary partnership of ethnographers and bioscientists from the University of Helsinki (Finland) and the University of Abomey-Calavi (Republic of Benin), collaborating on research into solutions of emerging global health concern of antimicrobial resistance (AMR). Drawing upon ongoing research and previous field experiences in relation to microbial solutions to infectious diseases, we discuss how Beninese onto-epistemologies resist microbial research but also offer opportunities for reflecting what a decolonial approach to collaborative microbiome research could be. While literature, and recommendations, on ethical indigenous microbiome research is mounting (see e.g Mangola 2022), there are few published examples how this would be done in practice, especially from across the African continent. This chapter aims to fill that gap.
Low-income regions such as Benin bear the greatest burden of infectious diseases globally, compounded with increasing antimicrobial resistance. Traditional medicine that is based on protection and healing either with foodstuffs, phytomedicines (medicines made of local plants), or protective amulets, plays a crucial role in Beninese primary healthcare, as it is more accessible and affordable than biomedicines. Based on this local knowledge, the region is seen to offer various innovative microbiological solutions that are gaining scientific attention. Beyond the more well-known examples of harvesting faeces, prominent domestic research centres have turned to indigenous fermented healing preparations as well as various phytomedicines as sources of new probiotic microbial strains, antimicrobial compounds as well as practices that might generate protective microbial ecologies.
Questions thus turn to inclusive Intellectual Property and legal assurances that African peoples will retain the rights to the pharmaceutical innovations developed from their medical heritage. Addressing these questions includes paying attention to the onto-epistemologies of the medical lineage itself, which can be mundane, but also ancestral, spiritual, and aggressively guarded. We present examples from our research with links to microbiome research: for example, the documenting the cosmological and spiritual agencies of microorganisms in traditional ferments; or evaluating antihelminth interventions that reveal the human-helminth relationship as one of careful curation and familial co-existence rather than outright eradication.
In our analysis of the encounters between the microbiological research and the intellectual property system on the one hand and traditional medicine as an onto-epistemological expert system as well as its elevation as a national healthcare and domestic research priority on the other, we pay attention to questions of ownership and guardianship, and African realities of health care access. We offer insights what health concerns take priority, how they are navigated, and the holding together of non-coherent (Law 2004) and at times antagonistic ways of knowing and being in the world. Such insights have value when approaching the question of how to conduct locally beneficial microbiome research in the region, and that can help to shape a decolonial microbiome science.
References:
Law, J. (2004). And if the Global Were Small and Noncoherent? Method, Complexity, and the Baroque. Environment and Planning D: Society and Space, 22(1), 13-26. https://doi.org/10.1068/d316t
Mangola, S.M., Lund, J.R., Schnorr, S.L. et al. (2022). Ethical microbiome research with Indigenous communities. Nature Microbiology, 7, 749–756. https://doi.org/10.1038/s41564-022-01116-w
Marta Scaglioni, Cà Foscari University of Venice
Negotiated Categories. The Co-Construction of the Tunisian Population in Human Microbiome Research and its Historical Entanglements
The analysis of the intersection between race and microbiome science is a growing area in the social sciences, primarily focusing on how racial discrimination and racism impact microbial diversity and how population categories, especially in Global South research, entail racialization (Maroney 2017; Zimmer 2019; Benezra, DeStefano, and Gordon 2012; Benezra 2020; De Wolfe et al. 2021; Nieves Delgado and Baedke 2021; Raffaetà 2022; Núñez Casal 2024; Rawson 2024; Nieves Delgado and Baedke 2024). However, little scholarly attention has been given to how these population categories are constructed, or how they intersect with or diverge from local conceptions of race. Drawing from prolonged ethnographic research on an EU-funded human microbiome project involving Italian and Tunisian researchers, this presentation argues that population categories in microbiome research are not merely imposed. Instead, they are continually negotiated and co-constructed with local, home-grown racial categories. Focusing on the construction of the Tunisian population, this article employs a historical lens to unveil the colonial historicity behind the scientific deployment of racial differences. To maintain this dual focus, the presentation addresses population categories in Tunisia as contextual, historically sedimented phenomena (Ahmed 2015). It will rely on anthropological literature on race in Tunisia (Pouessel 2012) and it will answer the social sciences’ call to analyze the historicity behind the use of racial differences in science (Meloni et al. 2022; Prasad 2023). This presentation challenges a simplistic dichotomy between Western, modern scientific typological thinking, often perceived as fixed—and pre-modern, local conceptions of race, frequently assumed to be fluid and changeable. It also unravels how race, within the epigenetic paradigm, is constituted by biological, cultural, and environmental deterministic ideas. The field has been carried out in 2023 and has comprised a stay at the Tunisian lab and in-depth interviews with the researchers involved.
Keywords: Tunisia, microbiome science, population categories, race, epigenetics.
References
Ahmed, Sara. 2015. ‘Race as Sedimented History’. Postmedieval: A Journal of Medieval Cultural Studies 6 (1): 94–97.
Benezra, Amber. 2020. ‘Race in the Microbiome’. Science, Technology, & Human Values 45 (5): 877–902.
Benezra, Amber, Joseph DeStefano, and Jeffrey I. Gordon. 2012. ‘Anthropology of Microbes’. Proceedings of the National Academy of Sciences 109 (17): 6378–81.
De Wolfe, Travis J., Mohammed Rafi Arefin, Amber Benezra, and María Rebolleda Gómez. 2021. ‘Chasing Ghosts: Race, Racism, and the Future of Microbiome Research’. Edited by Kathryn C. Milligan-Myhre. mSystems 6 (5): e00604-21.
Maroney, Stephanie. 2017. ‘Reviving Colonial Science in Ancestral Microbiome Research’. MicrobioSocial (blog). 2017. https://microbiosocial.wordpress.com/2017/01/10/reviving-colonial-science-in-ancestral-microbiome-research/.
Meloni, Maurizio, Tessa Moll, Ayuba Issaka, and Christopher W. Kuzawa. 2022. ‘A Biosocial Return to Race? A Cautionary View for the Postgenomic Era’. American Journal of Human Biology 34 (7): e23742.
Nieves Delgado, Abigail, and Jan Baedke. 2021. ‘Does the Human Microbiome Tell Us Something about Race?’ Humanities and Social Sciences Communications 8 (1): 1–12.
———. 2024. ‘How to Eliminate Race from Human Microbiome Research’. Università degli studi di Sassari.
Núñez Casal, Andrea. 2024. ‘Race and Indigeneity in Human Microbiome Science: Microbiomisation and the Historiality of Otherness’. History and Philosophy of the Life Sciences 46 (2): 17.
Pouessel, Stéphanie. 2012. Noirs au Maghreb: enjeux identitaires. Hommes et sociétés. Tunis Paris: IRMC Karthala.
Prasad, Amit. 2023. Science Studies Meets Colonialism. Cambridge Hoboken (N.J.): Polity Press.
Raffaetà, R. 2022. Metagenomic Futures: How Microbiome Research Is Reconfiguring Health and What It Means to Be Human. Abingdon, Oxon ; New York, NY: Routledge.
Rawson, Ariel Janaye. 2024. ‘Anti-Racism, Racism, and the Microbiome: A Review’. Progress in Environmental Geography 3 (2): 137–59.
Zimmer, Alexis. 2019. ‘Collecter, conserver, cultiver des microbiotes intestinaux: Une biologie du sauvetage’. Ecologie & politique N°58 (1): 135.
Elian Schure, Utrecht University
Sociocultural progress in gut microbiome research: a critical approach to the ‘transition’ narrative in South African gut microbiome research
The In gut microbiome research about South Africa, researchers often refer to the country as ‘ transitioning’ (Oduaran et al. 2020; Tamburini et al. 2022; Ramaboli et al. 2024). This transition is usually connected to the rise of non-communicable diseases, which reflects the ideas of the medical doctor and epidemiologist Abdel Omran. Omran (1971) introduced his seminal idea concerning the connection between a country’s modernisation and the rise of non-communicable diseases in the early 70s. Omran observes a shift from infectious diseases to non-communicable diseases as a country modernises. Over the last 50 years, Omran’s framework has gained considerable popularity and is used to model and explain the increasing prevalence of non-communicable diseases in various national and international contexts (Weisz and Olszynko-Gryn, 2010). He also inspired the creation of the ‘nutritional’ transition by the nutrition scholar Barry Popkin (1993) in the 90s. Despite the model’s frequent application, several scholars have critiqued Omran’s theory for not aligning with historical data and for being somewhat vague in its classification of certain diseases (see, amongst others, Mackenbach 2020). Furthermore, the model seemingly fails to accurately describe the situation in many African countries, where infectious diseases remain deadly while non-communicable diseases are on the rise (Peer 2015). The three stages of the epidemiological transition also imply that every country progresses through the same stages linearly, reinforcing that countries experience the same sociocultural progression at different moments in time (Nisbeth, 1970). Nevertheless, the epidemiological transition is often – directly or indirectly – cited in South African gut microbiome research to elucidate the national increase in obesity and cardiovascular diseases. I critically discuss the role the transition framework plays in gut microbiome research and demonstrate how the epidemiological transition is employed in gut microbiome research despite not accurately reflecting the South African context. I also critique the linear sociocultural progression that the transition narrative reiterates.
References
Mackenbach, J P. 2020. “Omran’s ‘Epidemiologic Transition’ 50 Years On.” International Journal of Epidemiology 51 (4): 1054–57.
Nisbet, R A. 1970. Social Change and History: Aspects of the Western Theory of Development. Repr. London, etc.: Oxford University Press.
Oduaran, O H, F B Tamburini, V Sahibdeen, R Brewster, F X Gómez-Olivé, K Kahn, S A Norris, et al. 2020. “Gut Microbiome Profiling of a Rural and Urban South African Cohort Reveals Biomarkers of a Population in Lifestyle Transition.” BMC Microbiology 20 (1): 330. https://doi.org/10.1186/s12866-020-02017-w.
Omran, A R. 1971. “The Epidemiologic Transition. A Theory of the Epidemiology of Population Change.” The Milbank Memorial Fund Quarterly 49 (4): 509–38.
Peer, Nasheeta. 2015. “The Converging Burdens of Infectious and Non-Communicable Diseases in Rural-to-Urban Migrant Sub-Saharan African Populations: A Focus on HIV/AIDS, Tuberculosis and Cardio-Metabolic Diseases.” Tropical Diseases, Travel Medicine and Vaccines 1 (1): 1–8. https://doi.org/10.1186/s40794-015-0007-4.
Popkin, Barry M. 1993. “Nutritional Patterns and Transitions.” Population and Development Review 19 (1): 138–57. https://doi.org/10.2307/2938388.
Ramaboli, M C, S Ocvirk, M Khan Mirzaei, B L Eberhart, M Valdivia-Garcia, A Metwaly, K Neuhaus, et al. 2024. “Diet Changes due to Urbanization in South Africa Are Linked to Microbiome and Metabolome Signatures of Westernization and Colorectal Cancer.” Nature Communications 15 (1): 3379. https://doi.org/10.1038/s41467-024-46265-0.
Tamburini, Fiona B, Godfred Agongo, Dylan Maghini, Ovokeraye H Oduaran, Ryan Brewster, Michaella R Hulley, Venesa Sahibdeen, et al. 2022. “Short- and Long-Read Metagenomics of Urban and Rural South African Gut Microbiomes Reveal a Transitional Composition and Undescribed Taxa.” Nature Communications 13 (1). https://doi.org/10.1038/s41467-021-27917-x.
Weisz, George, and Jesse Olszynko-Gryn. 2010. “The Theory of Epidemiologic Transition: The Origins of a Citation Classic.” Journal of the History of Medicine and Allied Sciences 65 (3): 287–326.
Susan V. H. Castro, Wichita State University
Ubuntu Revisited: Healing for a Microbiome-Inclusive Person
In this philosophical paper I outline how the general sub-Saharan ethical idea of Ubuntu, “I am because we are”, can ground a less Colonial approach to the role of microbiomics in African health than CRISPR and surgical alternatives. The key ideas that structure the paper are first, that microbiomes are communities to which we belong and which belong to us as part of our personhood: I am because we - my microbiome and me - are. Second, microbiomes are shareable within human communities: I am because we – we humans and our microbiomes – are. By reconceiving the Western pathogen-contagion model of disease to accurately reflect the role of microbiome transmission in ordinary community life through touching and food sharing practices, we can identify the processes of microbiome replenishment as a target for microbiome research. Third, a deeper understanding of microbiome ecology with Ubuntu and microbiome sharing in place can lead to the development of low-tech interventions that are effective, low risk, low cost, and minimize Western control and dependence. Finally, the disastrous history of Western ecological interventions, typically involving the introduction of a new species in an attempt to alter an ecosystem, speaks to the dangers of some of the high-tech interventions being developed, especially CRISPR editing of microbiomes.
To elaborate the core idea and its motivation very briefly, Jennifer Doudna introduced her vision of using CRISPR to edit our microbiomes to cure Crohn’s Disease and other microbiomial disorders, promoting this as the better alternative to fecal transplants. She has since established the Berkeley Initiative for Optimized Microbiome Editing (BIOME) in pursuit of this vision. This is obviously a high-tech, high-cost solution with significant biocontainment risks and unknown side effects. Western aid and development initiatives historically applied to African concerns typically offer high-tech, low cost solutions subject to Western control. These are Colonial models to the extent that Western control of the technology, the expertise required to use it, and the means of production are ineliminable. Fecal transplants are a lower-tech treatment for Crohn’s Disease with little biocontainment risk and well understood risks to the patient, yet dangerous in their own right with additional antibiotic load.
Taking an Ubuntu approach to microbiome intervention, our microbiomes are part of us, communities of living things, and a shared resource for flourishing and survival. Microbiome sharing occurs in vaginal births when infants come into contact with both vaginal and fecal microbiomes. It occurs in casual contacts when people offer physical affection and comfort, or engage in grooming practices such as communal bathing and hair braiding. It occurs in food sharing practices when people eat from the same plate and pass food from hand to hand. In all of these practices, social bonding is accompanied by microbiome sharing that can replenish and rebalance what individuals may have lost through irregular diet, illness, or even use of antibiotics. This Ubuntu approach does depend in part on high-tech microbiome research, but it does so primarily for insight, diagnosis, and monitoring rather than as a means of intervention.
Yolandi Coetser (North West University) & Nicolae Morar (University of Oregon)
Malnutrition, Gut Microbiome, and Environmental Justice in South Africa
The question of malnutrition remains one of the most significant bioethical challenges of our time. In 2022, as the WHO notes, nearly 2.5 billion adults were either overweight or underweight, and about 149 million children under the age of 5 were too short for their age (stunted) and 45 million too thin for their age. In bioethics, the question of malnutrition is often framed in medical terms since it is supposed to characterize deficiencies or imbalances in a person’s diet, as it pertains to their energy intake or diversity of nutrients. In this paper, we investigate the problem of malnutrition in South Africa and its impact on its population, where 23% of children experience severe food poverty (UNICEF). It is worth noting that food poverty can not only be caused, but also exasperated by environmental crises, such as pollution and lack of fresh food due to extreme weather events. We are interested not only in the overall health impact on such populations, but also on their drastic effects on gut microbiome composition and on the long-term effects on development. For this reason, we intend to complement the medical framework by adding an environmental justice lens, which aims to highlight the importance of equal access to healthy environments and food security.